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Running Thor over MyGrid

Running Thor over MyGrid. Walfredo Cirne Universidade Federal de Campina Grande. Thor. Thor is a Molecular Modelling package It simulates the molecular movement of atoms and molecules It determines the lower energy configuration of the system It was developed at UFRJ (Paulo Bisch´s team).

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Running Thor over MyGrid

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  1. Running Thor over MyGrid Walfredo Cirne Universidade Federal de Campina Grande

  2. Thor • Thor is a Molecular Modelling package • It simulates the molecular movement of atoms and molecules • It determines the lower energy configuration of the system • It was developed at UFRJ (Paulo Bisch´s team)

  3. Fighting AIDS with Thor • HIV virus mutates at a fast pace • Regional variants are emerging • We would like to better understand the drugs effect on the Brazilian HIV variant • We need to run a Thor parameter sweep, varing the HIV variant and the inhibitor • Thor is used to simulate the inhibitor/protease interaction

  4. Bag-of-Tasks Applications • Parallel applications whose tasks are independent • Data mining • Massive search (as search for crypto keys) • Parameter sweeps • Monte Carlo simulations • Fractals (such as Mandelbrot) • Image manipulation (such as tomography) • And many others…

  5. The Motivation for MyGrid • Users of loosely-coupled applications could benefit from the Grid now • However, they don´t run on the Grid today because the Grid Infrastructure is not widely deployed • What if we build a solution that does not depend upon installed Grid infrastructure?

  6. MyGrid Scope • MyGrid allows a user to run Bag-of-Tasks parallel applications on whatever resources she has access to • Bag-of-Tasks applications are those parallel applications formed by independent tasks • One’s grid is all resources one has access to • No grid infrastructure software is necessary • Grid infrastructure software can be used (whenever available)

  7. What is MyGrid? • MyGrid is a framework to build and run BoT applications on user-defined grids • The user provides: • A description of her Grid • A way to do remote execution and file transfer • “The application” • MyGrid provides: • Grid abstractions • Scheduling

  8. Simple MyGrid Example # initial mg-services mirror $PROC tarefa mg-services put $PROC ENTRADA.$TASK $PLAYPEN # grid tarefa < ENTRADA.$TASK > SAÍDA # final mg-services get $PROC $PLAYPEN/SAÍDA resultados/SAÍDA.$TASK

  9. Defining My Personal Grid proc:name = ostra.lsd.ufcg.edu.br attributes = lsd, linux type = user_agent proc:name = memba.ucsd.eduattributes = lsd, solaristype = grid_script rem_exec = ssh %machine%command copy_to = scp %localdir/%file %machine:%remotedir copy_from = scp %machine:%remotedir/%file %localdir [...]

  10. Factoring with MyGrid • Fatora n generates files tasks, init, gridi, and collect, and then invokes mg-addtask tasks • tasks task: init= init grid= grid1 final= collect task: init= init grid= grid2 …

  11. Factoring with MyGrid • initmg-services put $PROC ./Fat.class $PLAYPEN • grid1java Fat 3 18655 34789789798 output-$TASK • grid2 java Fat 18655 37307 34789789798 output-$TASK • collect mg-services get $PROC $PLAYPEN/output-$TASK results

  12. HomeMachine Scheduler Grid Machine Interface Globus Proxy UA Proxy GridScript ... Grid Machine Grid Machine Grid Machine Globus GRAM UserAgent ... Making MyGrid Encompassing

  13. Scheduler (Home Mac.) User Agent Grid Script Globus Proxy Grid Machine Gateway Space-Shared Gateway Dealing with Firewalls, Private IPs, and Space-Shared Machines

  14. The Scheduling Challenge • Grid scheduling typically depends on information about the grid (e.g. machine speed and load) and the application (e.g. task size) • However, getting grid information makes it harder to build an encompassing system • The Grid Machine Interface would have to be richer, and thus harder to implement • Moreover, getting application information makes the system harder to use and less simple • The user would have to provide task size estimates

  15. Scheduling With No Information • Work-queue with Replication • Tasks are sent to idle processors • When there are no more tasks, running tasks are replicated on idle processors • The first replica to finish is the official execution • Other replicas are cancelled • Replication may have a limit • The key is to avoid having the job waiting for a task that runs in a slow/loaded machine

  16. Work-queue with Replication • 8000 experiments • Experiments varied in • grid heterogeneity • application hetetogeneity • application granularity • Performance summary:

  17. Application Granularity

  18. Grid Heterogeneity

  19. WQR Overhead • Obviously, the drawback in WQR is cycles wasted by the cancelled replicas • Wasted cycles:

  20. Application Granularity

  21. Proof of Concept • During a 40-day period, we ran 600,000 simulations using 178 processors located in 6 different administrative domains widely spread in the USA • We only had GridScript and WorkQueue • MyGrid took 16.7 days to run the simulations • My desktop machine would have taken 5.3 years to do so • Speed-up is 115.8 for 178 processors

  22. Fighting AIDS • 55 machines in 6 administrative domains in the US and Brazil • The machines were accessed via User Agent, UA + Grid Machine Gateway, UA + ssh tunnel, and Grid Scripts • Task = 3.3 MB input, 200 KB output, 4 to 33 minutes of dedicated execution • Ran 60 tasks in 38 minutes • Speed-up is 29.2 for 55 machines • Considering an 18.5-minute average machine

  23. Conclusions • Bag-of-tasks parallel applications can currently benefit from the Grid • Running grid applications at the user-level is a viable strategy • However, firewalls, private IPs and the such make it much harder than we initially thought • Is “upperware” the way to go for new middleware development?

  24. Future Work • Make MyGrid OGSA-complaint • Create OurGrid, a community grid for resource sharing • Extend the scheduler for data intensive applications • Such a scheduler should try to minimize data movement

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